Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes.

The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.

Human occupations and climate change in the Puna de Atacama, Chile.

Widespread evidence for human occupation of the Atacama Desert, 20 degrees to 25 degrees S in northern Chile, has been found from 13,000 calibrated 14C years before the present (cal yr B.P.) to 9500 cal yr B.P., and again after 4500 cal yr B.P. Initial human occupation coincided with a change from very dry environments to humid environments. More than 39 open early Archaic campsites at elevations above 3600 meters show that hunters lived around late glacial/early Holocene paleolakes on the Altiplano. Cessation of the use of the sites between 9500 and 4500 cal yr B.P. is associated with drying of the lakes. The mid-Holocene collapse of human occupation is also recorded in cave deposits. One cave contained Pleistocene fauna associated with human artifacts. Faunal diversity was highest during the humid early Holocene.